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References

  • Ahn S, Tanksley SD. 1993. Comparative linkage maps of the rice and maize genomes. Proceedings of the National Academy of Sciences, USA 90: 79807984.
  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Research 25: 33893402.
  • Anderson E. 1945. What is Zea mays? A report of progress. Chronicle of Botany 9: 8892.
  • Bennetzen JL, Ramakrishna W. 2002. Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Molecular Biology 48: 821827.
  • Blanc G, Hokamp K, Wolfe KH. 2003. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Research 13: 137144.
  • Bowers JE, Chapman BA, Rong J, Paterson AH. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433438.
  • Carels N, Bernardi G. 2000. Two classes of genes in plants. Genetics 154: 18191825.
  • Devos KM, Gale MD. 2000. Genome relationships: the grass model in current research. Plant Cell 12: 637646.
  • Feuillet C, Keller B. 2002. Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Annals of Botany 89: 310.
  • Gale MD, Devos KM. 1998. Comparative genetics in the grasses. Proceedings of the National Academy of Sciences, USA 95: 19711974.
  • Gaut BS. 2002. Evolutionary dynamics of grass genomes. New Phytologist 154: 1528.
  • Gaut BS, Doebley JF. 1997. DNA sequence evidence for the segmental allotetraploid origin of maize. Proceedings of the National Academy of Sciences, USA 94: 68096814.
  • Gaut BS, Morton BR, McCaig BC, Clegg MT. 1996. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proceedings of the National Academy of Sciences, USA 93: 1027410279.
  • Ge S, Sang T, Lu BR, Hong DY. 1999. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proceedings of the National Academy of Sciences, USA 96: 1440014405.
  • Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92100.
  • Helentjaris T, Weber D, Wright S. 1988. Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics 118: 353363.
  • Huang S, Sirikhachornkit A, Su X, Faris J, Gill B, Haselkorn R, Gornicki P. 2002. Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proceedings of the National Academy of Sciences, USA 99: 81338138.
  • Jacobs BF, Kingston JD, Jacobs LL. 1999. The origin of grass-dominated ecosystems. Annals of the Missouri Botanical Garden 86: 590643.
  • Kellogg EA. 2001. Evolutionary history of the grasses. Plant Physiology 125: 11981205.
  • Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y, Yasunishi A. 2003. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301: 376379.
  • Lawrence WJC. 1931. The secondary association of chromosomes. Cytologia 2: 352384.
  • Levy AA, Feldman M. 2002. The impact of polyploidy on grass genome evolution. Plant Physiology 130: 15871593.
  • Li WH. 1997. Molecular evolution. Sunderland, MA, USA: Sinauer Associates.
  • Martienssen RA, Rabinowicz PD, O'Shaughnessy A, McCombie WR. 2004. Sequencing the maize genome. Current Opinion in Plant Biology 7: 102107.
  • Moore G, Devos KM, Wang Z, Gale MD. 1995. Cereal genome evolution: grasses, line up and form a circle. Current Biology 5: 1995.
  • Nayar NM. 1973. Origin and cytogenetics of rice. Advances in Genetics 17: 153292.
  • Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3: 418426.
  • Ozkan H, Levy AA, Feldman M. 2001. Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops–Triticum) group. Plant Cell 13: 17351747.
  • Paterson AH, Bowers JE, Peterson DG, Estill JC, Chapman BA. 2003. Structure and evolution of cereal genomes. Current Opinion in Genetics and Development 13: 644650.
  • Paterson AH, Bowers JE, Chapman BA. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proceedings of the National Academy of Sciences, USA 101: 99039908.
  • Seoighe C. 2003. Turning the clock back on ancient genome duplication. Current Opinion in Genetics and Development 13: 636643.
  • Simillion C, Vandepoele K, Saeys Y, Van De Peer Y. 2004. Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Research. 14: 10951106.
  • Stebbins GL. 1971. Chromosomal evolution in higher plants. London, UK: Edward Arnold.
  • Stebbins GL. 1981. Coevolution of grasses and herbivores. Annals of the Missouri Botanical Garden 68: 7586.
  • Thompson JD, Higgins DG, Gibson TJ. 1994. clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 46734680.
  • Vandepoele K, Simillion C, Van De Peer Y. 2003. Evidence that rice and other cereals are ancient aneuploids. Plant Cell 15: 21922202.
  • Vaughan DA, Morishima H, Kadowaki K. 2003. Diversity in the Oryza genus. Current Opinion in Plant Biology 6: 139146.
  • Wilson WA, Harrington SE, Woodman WL, Lee M, Sorrells ME, McCouch SR. 1999. Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize and the domesticated panicoids. Genetics 153: 453473.
  • Wolfe KH. 2001. Yesterday's polyploids and the mystery of diploidization. Nature Reviews Genetics 2: 333341.
  • Wolfe KH, Li WH, Sharp PM. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences, USA 84: 90549058.
  • Yang Z. 1997. paml: a program package for phylogenetic analysis by maximum likelihood. Computer Applications in the Bioscience 13: 555556.
  • Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 7992.
  • Zhao W, Wang J, He X, Huang X, Jiao Y, Dai M, Wei S, Fu J, Chen Y, Ren X, Zhang Y, Ni P, Zhang J, Li S, Wang J, Wong GK, Zhao H, Yu J, Yang H, Wang J. 2004. BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Research 32(Database issue): D377–D382.